 Nate Coraor
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705457f218
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Convert DOS line endings.
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2013-10-10 12:48:07 -04:00 |
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John Chilton
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b83f3a7e96
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Backout of c78f3f687fbc. I'm sure it is fine, but @natefoo got in my head and I don't want to break anything.
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2013-10-10 11:16:20 -05:00 |
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Daniel Blankenberg
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61bb975d6c
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Add status code 404 to response in tool_runner when a tool does not exist.
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2013-10-10 11:45:42 -04:00 |
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Daniel Blankenberg
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1f78b99b10
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Remove test/unit/test_tool_loader.pyc added in 10286:edef166c163f.
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2013-10-10 10:58:47 -04:00 |
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Daniel Blankenberg
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f2407f52e3
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Fix for DiskObjectStore Docstring unit test.
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2013-10-10 10:54:34 -04:00 |
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Nate Coraor
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6a99bac16a
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Temporarily remove graph datatypes (necessary to avoid autodetection problems) until their sniffers are fixed. See also: a60d756aeb5d
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2013-10-10 10:42:56 -04:00 |
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Greg Von Kuster
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5ba8370e85
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Fixes and code cleanup for installing tool dependencies defined in tool shed repository definition file via fabric.
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2013-10-10 10:35:37 -04:00 |
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Daniel Blankenberg
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186da8657e
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Add Pythonic FASTQ to FASTA converter back into tool_conf.xml.main removed in 10720:870b10eaa4cf.
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2013-10-10 10:00:13 -04:00 |
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John Chilton
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3f628bf544
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Refactor job status checking logic into its own module.
Add unit tests for some basic behaviors.
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2013-10-10 00:17:17 -05:00 |
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Martin Cech
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63cf00c514
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user activation flow tweaked, link at the masthead message providing activation resending
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2013-10-09 15:12:36 -04:00 |
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John Chilton
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2d1d284384
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Fix stdio return code handling that has been broken for a few releases.
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2013-10-09 12:48:26 -05:00 |
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Greg Von Kuster
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006317a42e
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Code cleanup for defining and building repository dependency relationships when installing tool shed repositories into Galaxy and fixes for handling Galaxy tool panel section selection when installing repository dependencies.
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2013-10-09 13:33:31 -04:00 |
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Daniel Blankenberg
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dd5de722f2
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Fix and enhance admin/view_tool_data_tables.
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2013-10-09 12:01:54 -04:00 |
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Daniel Blankenberg
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1038798d6e
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Fix for lib/galaxy/datatypes/converters/fastq_to_fqtoc.py
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2013-10-09 10:52:36 -04:00 |
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Daniel Blankenberg
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58fd85a4af
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Remove references to g2.trac.bx.psu.edu. Several references still exist in rgenetics converter tools and rgenetics test-data.
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2013-10-09 10:50:05 -04:00 |
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Dave Bouvier
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c57f223f35
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Prevent duplicate lines from being written to an env.sh file when installing a tool dependency or re-running a tool migration script with tool dependencies specified to be installed.
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2013-10-08 16:48:05 -04:00 |
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Jeremy Goecks
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ba2c357a56
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Fixes for 82b1789: (a) incorporate default values correctly and (b) use Backbone-style gets to access config values.
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2013-10-08 12:25:10 -04:00 |
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Aysam Guerler
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2edc2ad9e1
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Update modal and upload
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2013-10-08 12:12:48 -04:00 |
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Greg Von Kuster
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949edb0d88
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Fix for automatically populating the changeset revision in a repository_dependencies..xml file for defined dependencies that are circular.
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2013-10-08 11:56:00 -04:00 |
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Jeremy Goecks
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172878e697
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Trackster: small fixes for calculating tile height.
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2013-10-08 11:45:49 -04:00 |
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Dave Bouvier
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fbad610b2b
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Fix for a bug introduced with the rename_to option for the move_file action.
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2013-10-08 11:12:10 -04:00 |
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Jeremy Goecks
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7a4f426a64
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Trackster: make DrawableConfig into a Backbone model and consolidate rendering into a Backbone view.
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2013-10-08 10:55:43 -04:00 |
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Carl Eberhard
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69559512b0
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History panel: better reconciling of hda states within history and hda collection
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2013-10-08 10:47:43 -04:00 |
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Ross Lazarus
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5d4e73cc1e
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Proper removal of rgenetics deprecated tool wrappers
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2013-10-08 16:30:54 +11:00 |
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Ross Lazarus
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b467ec50bb
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Big cleanup - remove material in tools/rgenetics accidentally added in August when a push was made from a BakerIDI repository - apologies to all. This push will revert all those changes and also removes the old rgenetics SNP tools which are now deprecated.
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2013-10-08 16:15:56 +11:00 |
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Ross Lazarus
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620ed52930
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restore original tools/actions/__init__.py
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2013-10-08 13:39:22 +11:00 |
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Ross Lazarus
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c1af859f90
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revert bowtie2 and tophat2 wrappers
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2013-10-08 13:34:54 +11:00 |
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Ross Lazarus
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93c3148b4c
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backout -r 10811
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2013-10-08 10:56:03 +11:00 |
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Ross Lazarus
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8c4f96ed81
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backout -r 10808
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2013-10-08 10:55:24 +11:00 |
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Ross Lazarus
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4caf74eaa6
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backout -r 10806
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2013-10-08 10:54:45 +11:00 |
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Ross Lazarus
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66b690d599
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backout -r 10802
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2013-10-08 10:53:45 +11:00 |
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Ross Lazarus
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070ee188fa
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backout -r 10800
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2013-10-08 10:52:21 +11:00 |
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Ross Lazarus
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eaaaa3cce7
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backout -r 10799
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2013-10-08 10:50:10 +11:00 |
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Ross Lazarus
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a17e071f38
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hg backout -r 1092b0d
backout unintended commits to tophat and bowtie2 wrappers
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2013-10-08 10:24:59 +11:00 |
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Daniel Blankenberg
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45d1895739
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Pack scripts
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2013-10-07 17:00:29 -04:00 |
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Daniel Blankenberg
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679ebd5746
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Fix for history updater when setting metadata
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2013-10-07 17:00:22 -04:00 |
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Dave Bouvier
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2cd5ccd4ad
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Fix for update manager functional test failing.
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2013-10-07 16:46:17 -04:00 |
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Greg Von Kuster
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2d6417b5a8
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Fix javascript function to check all check boxes for select lists in the tool shed and Galaxy that handle resetting metadata on selected repositories and installing and uninstalling selected tool dependencies.
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2013-10-07 16:35:38 -04:00 |
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Daniel Blankenberg
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0ddc8d3a3d
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Fix for auto-detect metadata tool running second set metadata call.
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2013-10-07 16:27:08 -04:00 |
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Jeremy Goecks
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570134a838
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Automated merge
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2013-10-07 16:17:45 -04:00 |
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Dave Bouvier
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d3cea0e05d
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Make extract_log_data return a list of dicts rather than a dict.
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2013-10-07 14:28:43 -04:00 |
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Greg Von Kuster
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ec3b16e8bf
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Allow tool dependencies with a status of NEVER_INSTALLED to be installed.
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2013-10-07 12:48:25 -04:00 |
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Jeremy Goecks
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770c323b8d
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Add close button to Trackster.
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2013-10-07 12:36:34 -04:00 |
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Dannon Baker
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7c12eee279
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Revert addition GALAXY_RUN_ALL=1 in run.sh
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2013-10-07 11:14:25 -04:00 |
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Greg Von Kuster
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d516842c08
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Fix setting mimetype for image files in tool shed repositories.
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2013-10-07 10:32:33 -04:00 |
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Greg Von Kuster
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8ba7578b10
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Set mimetype when displaying images in tool shed repositories.
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2013-10-07 10:14:42 -04:00 |
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Dave Bouvier
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892954a937
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Reimplement fix for some tarballs that incorrectly result in an error state when they attempt to create symlinks to files that do not exist on the destination filesystem.
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2013-10-07 08:59:31 -04:00 |
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Ross Lazarus
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59bd638b82
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updated ucsc builds
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2013-10-07 10:41:50 +11:00 |
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Ross Lazarus
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87b1203b4a
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branch merge
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2013-10-05 09:56:05 +10:00 |
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Ross Lazarus
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7938d1fc81
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local changes
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2013-10-05 09:51:18 +10:00 |
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